Definitive biodistribution maps that establish the interdependency of the size, shape, deformability and surface chemistry of nanoparticles in vitro and in vivo over length scales ranging from cells to tissues to the entire organism are needed by many different research communities. Environmental regulators, pulmonologists, oncologists, pharmaceutical scientists, toxicologists, cell biologists and dermatologists all need definitive answers related to particle biodistributions, particle permeability and transport using “calibration quality” particles. For example, fungal and bacterial pathogens are first and foremost recognized by their form or shape; however, the complete understanding of the role and significance of that form and shape is largely lacking. Indeed, some rod-like bacterial pathogens, including the gram-negative bacteria Salmonella, Shigella, and Yersinia and the gram-positive bacterium Listeria monocytogenes can induce their entry into non-phagocytic mammalian cells. Likewise, red blood cells and neutrophils are able to deform and undergo over 100 % strain (double in length) in order to navigate through various biological barriers that would prevent non-flexible objects from crossing. As such, nanofabricated tools (e.g. precisely defined particles) hold significant promise to provide insight into the fundamentals of cellular and biological processes. These tools can also yield essential insights into the design of effective vectors for use in nanomedicine, especially for the design of nanoparticles for use as targeted therapeutics and imaging agents. Indeed, very little is known about how the interdependency of size, shape, deformability and surface chemistry can influence the biodistribution, cell-uptake, and intra-cellular trafficking of micro- and nanoparticles. Beyond understanding the biodistribution of particles delivered via parenteral routes, particle size, shape, deformability and surface chemistry should play a very significant role for understanding the mechanisms associated with particles that are inhaled, either intentionally for use as a therapeutic or during environmental exposure. Understanding the role that mechano-biology plays as a function of size, shape and surface chemistry certainly lies at the core of how biological particles like neutrophils and red blood cells navigate their barriers. Ascertaining definitive biodistribution maps through the use of precisely defined particle probes containing appropriate imaging beacons useful for quantification will undoubtedly lead to a set of rules that will be of immense use to science and to the application of nano-carriers to improve human health, treatment and diagnosis.